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Table 1 Comparison of tag quality between Peaks and PepNovo+, using Proteome Discoverer ™ peptide identifications as the expected sequences

From: Peptimapper: proteogenomics workflow for the expert annotation of eukaryotic genomes

Peaks Proteome discoverer
(MASCOT identifications)
Pepnovo+
ID Tag sequence Significant score >60% Rank Protein AC Reference Sequence e-value ID Tag sequence Significant score >1,5
271 WVQAAGAGASR 23 0 Esi0085_0010 SVVQAAGAGDAK 5,65568E-06 Spectrum271_scans QAAGAGA 6,346
271 WVQAAGAGWK 21.5 1
271 WVQAAGAGTGR 18.5 2
552 (CamC)VGVSEETTTRHR 31 0 Esi0091_0058 cVGVSEETTTGVHR 2,36909E-07 Spectrum552_scans GVSEDD 4,237
552 QMGVSEETTTRHR 29 1
552 V(CamC)GVSEETTTRHR 17 2
577 QFAGDDAPR 43 0 Esi0203_0038 AGFAGDDAPR 1,69937E-06 Spectrum578_scans GDDAPR 7,539
577 K(MetOxM)AGDDAPR 41 1
577 AGFAGDDAPR 11.5 2
642 KAENPMSKR 100 0 Esi0349_0012 KAEDIDTIR 1,01272E-05 Spectrum643_scans DLDTLR 4,727
642 KAQDPMSKR 0.1 1
642 QAKDPMSKR 0.02 2
1118 DGLVYGK(MetOxM)NEPPGAR 38 0 Esi0327_0021 ATLVYGQmNEPPGAR 2,42457E-06 Spectrum1119_scans EPPGAR 1,396
1118 DGLVYGQFNEPPGAR 37 1
1118 DGLVYGQ(MetOxM)NEPPGVK 8 2
2462 DESAAVFAWK 87,5 0 Esi0091_0058 DESAAVFAWK 1,64304E-05 Spectrum2463_scans SAAVFA 4,78
2462 DESAAVFAGTR 8 1
2462 LMSAAV(MetOxM)AGEK 1.5 2
2479 MDDLTNNALARK 58 0 Esi0888_0002 mVDLTPMAIAAGR 4,70366E-07 Spectrum2480_scans ALAAGR 1,943
2479 (MetOxM)VDLTNNALAAGR 39.5 1
2479 MDDLTNGGALARK 1 2
2558 ED(MetOxM)ETE(CamC)AVNYDNLYQVMK 48 0 Esi0349_0012 TccEAEcAVNYDNLYQAMR 1,01272E-05 Spectrum2559_scans VNYDNL 2,289
2558 DE(MetOxM)ETE(CamC)AVNYDNLYQVMK 8.5 1
2558 ED(MetOxM)ETE(CamC)AVNYDNLYQMVK 8 2
2610 TFQAGEVASALLGR 32 0 Esi0327_0021 FTQAGAEVSALLGR 5,99619E-08 Spectrum2610_scans SALLGR 4,356
2610 FTQAGEVASALLGR 25 1
2610 TFKAGAGNGSALLGR 10 2
3191 VALTGLTLAEYFR 53 0 Esi0327_0021 VALTGLTIAEYFR   Spectrum3196_scans LAEYFR 4,471
3191 GLLTGLTLAEYFR 25.5 1
3191 AVLTGLTLAEYFR 11 2
  1. The Peaks and Pepnovo + results are shown in the first and the last columns, with the Proteome Discoverer ™ identifications in between as reference sequences. We ran Peaks, PepNovo+, and Proteome Discoverer ™ on the top 10 high-quality selected spectra. Each spectrum corresponds to one row in the table. Sequences shown in bold are the correct sequences, thus four for Peaks and eight for PepNovo+